摘要
      关于集约化畜牧场是否可能构成临床相关抗微生物耐药性（AMR）的宿主，从而对周围社区构成威胁，目前正在进行辩论。在这里，我们结合了鸟枪宏基因组测序、机器学习（ML）和基于培养的方法，重点研究了中国的一个家禽养殖场和相连的屠宰场，调查了牲畜、工人及其家庭的肠道微生物组，以及尸体和土壤中的微生物群落。在这项研究中，微生物组和耐药性在不同环境和宿主之间都存在差异。然而，在更精细的范围内，在人类和肉鸡样本中都发现了几个类似的临床相关抗微生物耐药性基因（ARGs）和类似的相关移动遗传元件。接下来，我们重点关注大肠杆菌，这是农场AMR监测的一个重要指标。人们发现人和鸡之间混合有大肠杆菌菌株。我们观察到，鸡粪便耐药性组中存在的几种ARG与从相同样本培养的大肠杆菌分离株的耐药性/易感性谱相关。最后，通过使用环境传感，发现这些ARG与环境温度和湿度的变化有关。我们的研究结果表明，在复杂、相互关联的环境中研究微生物群落和AMR时，采用多领域和多尺度方法的重要性。
Abstract
A debate is currently ongoing as to whether intensive livestock farms may constitute reservoirs of clinically relevant antimicrobial resistance (AMR), thus posing a threat to surrounding communities. Here, combining shotgun metagenome sequencing, machine learning (ML), and culture-based methods, we focused on a poultry farm and connected slaughterhouse in China, investigating the gut microbiome of livestock, workers and their households, and microbial communities in carcasses and soil. For both the microbiome and resistomes in this study, differences are observed across environments and hosts. However, at a finer scale, several similar clinically relevant antimicrobial resistance genes (ARGs) and similar associated mobile genetic elements were found in both human and broiler chicken samples. Next, we focused on Escherichia coli, an important indicator for the surveillance of AMR on the farm. Strains of E. coli were found intermixed between humans and chickens. We observed that several ARGs present in the chicken faecal resistome showed correlation to resistance/susceptibility profiles of E. coli isolates cultured from the same samples. Finally, by using environmental sensing these ARGs were found to be correlated to variations in environmental temperature and humidity. Our results show the importance of adopting a multi-domain and multi-scale approach when studying microbial communities and AMR in complex, interconnected environments.

https://www.nature.com/articles/s41396-022-01315-7